I recently got that big box set, and the series really does go downhill fast after season 4. Season 5 still has a fair share of good eps, but after that, it's like a wasteland, with only a scant few noteworthy episodes per season. Usually when an ep is good though, it's REALLY good. The just chose to focus too much on the borderline incoherent conspiracy.
Serialized dramas have learned a lot of lessons over the past 2 decades, and th X-Files was the source for learning a lot of those lessons. Buffy for the most part took a bit of the X-Files formula and introduced seasonlong arcs. I'd like to see a new X-Files series do that. Either that, or go the Doctor Who route where there is continuity, but it isn't all that important. X-Files went with a SERIES-long arc, and unfortunately, it wasn't planned from the beginning, so it just ended up a terrible mess. Maybe a new series can take a cue from Lost, and plan the arc from the beginning, and end the series when it's supposed to end.